[petsc-users] DMPlex with spring elements

[Abhyankar, Shrirang G.]

My reply was based on the assumption that the values set at a vertex do
not have contributions from other vertices or edges. In which case, you
would not want to set any value for the ghost vertex.

For example, consider the following network

v1        e1       v2        e2       v3
| ---------------- | --------------- |

that gets distributed on two processors as follows

     v1     e1        v2'
[0]  | --------------- |

      v2        e2         v3
[1]   | ----------------- |


Here, v2' is the ghost vertex on P0. Now, if you want to set f(v2) = 2,
then you do not need to set anything for f(v2') and call DMLocalToGlobal()
at the end with INSERT_VALUES flag (You can also use ADD_VALUES flag
assuming that you have zeroed the local vector initially). On the other
hand, if you have f(v2) = f(v1) + f(v3) then you would need to set f(v2')
= f(v1) and f(v2) = f(v3) and call DMLocalToGlobal with the flag
ADD_VALUES.

Shri



From:  Miguel Angel Salazar de Troya <salazardetroya at gmail.com>
Date:  Tue, 30 Sep 2014 11:35:31 -0500
To:  Shri <abhyshr at mcs.anl.gov>
Cc:  "petsc-users at mcs.anl.gov" <petsc-users at mcs.anl.gov>
Subject:  Re: [petsc-users] DMPlex with spring elements


>No worries. Thanks for your responses. I'm assuming you suggested to use
>DMNetworkIsGhostVertex() and not modify its value for the case in which I
>were using the global vectors and not the local vectors, where it is
>possible, as Matt suggested.
>Miguel
>
>
>On Tue, Sep 30, 2014 at 11:22 AM, Abhyankar, Shrirang G.
><abhyshr at mcs.anl.gov> wrote:
>
>
>From:  Miguel Angel Salazar de Troya <salazardetroya at gmail.com>
>Date:  Mon, 29 Sep 2014 16:55:14 -0500
>To:  Shri <abhyshr at mcs.anl.gov>
>Cc:  "petsc-users at mcs.anl.gov" <petsc-users at mcs.anl.gov>
>Subject:  Re: [petsc-users] DMPlex with spring elements
>
>
>>Hi all
>>I'm bumping this post because I have more questions related to the same
>>problem.
>>
>>I am looping over the edges of my DMNetwork, then I obtain the vertices
>>that make up each edge with DMNetworkGetConnectedNode(). Each of these
>>vertices have two variables (or actually, two degrees of freedom for my
>>problem). My intentions are to modify the solution vector entries that
>>are affected by these variables in each vertex. I would call the function
>>DMNetworkGetVariableOffset() to do this. What happens if one of the
>>vertices is a ghost vertex? Can I still modify the solution vector? My
>>problem is that the edge has information to provide to these nodes.
>>
>>
>
>Sorry for the delay. I think you would want to use
>http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMNetworkIs
>G
>hostVertex.html and not modify the value for the ghost vertex.
>
>Shri
>
>>
>>Thanks
>>Miguel
>>
>>
>>
>>On Fri, Sep 26, 2014 at 12:33 PM, Miguel Angel Salazar de Troya
>><salazardetroya at gmail.com> wrote:
>>
>>I understand. Thanks a lot.
>>Miguel
>>
>>
>>On Fri, Sep 26, 2014 at 10:53 AM, Abhyankar, Shrirang G.
>><abhyshr at mcs.anl.gov> wrote:
>>
>>What Matt is saying is that there are two interfaces in PETSc for setting
>>the residual evaluation routine:
>>
>>i) SNESSetFunction takes in a function pointer for the residual
>>evaluation
>>routine that has the prototype
>>                 PetscErrorCode xyzroutine(SNES snes, Vec X, Vec F, void*
>>ctx);
>>
>>X and F are the "global" solution and residual vectors. To compute the
>>global residual evaluation, typically one does -- (a) scattering X and F
>>onto local vectors localX and localF (DMGlobalToLocal), (b) computing the
>>local residual, and (c) gathering the localF in the global F
>>(DMLocalToGlobal). This is what is done in the example.
>>
>>ii) DMSNESSetFunctionLocal takes in a function pointer for the residual
>>evaluation routine that has the prototype
>>                 PetscErrorCode xyzlocalroutine(DM, Vec localX, localF,
>>void* ctx)
>>
>>In this case, the localX and localF get passed to the routine. So, you
>>only have to do the local residual evaluation. PETSc does the
>>LocalToGlobal gather to form the global residual.
>>
>>I chose to use SNESSetFunction in the example. You can use either of
>>them.
>>
>>Shri
>>
>>From:  Matthew Knepley <knepley at gmail.com>
>>Date:  Fri, 26 Sep 2014 10:28:26 -0500
>>To:  Miguel Angel Salazar de Troya <salazardetroya at gmail.com>
>>Cc:  Jed Brown <jed at jedbrown.org>, Shri <abhyshr at mcs.anl.gov>,
>>"petsc-users at mcs.anl.gov" <petsc-users at mcs.anl.gov>
>>Subject:  Re: [petsc-users] DMPlex with spring elements
>>
>>
>>>On Fri, Sep 26, 2014 at 10:26 AM, Miguel Angel Salazar de Troya
>>><salazardetroya at gmail.com> wrote:
>>>
>>>Yeah, but doesn't it only work with the local vectors localX and localF?
>>>
>>>
>>>
>>>I am telling you what the interface for the functions is. You can do
>>>whatever you want inside.
>>>
>>>  Matt
>>>
>>>
>>>Miguel
>>>
>>>On Fri, Sep 26, 2014 at 10:10 AM, Matthew Knepley <knepley at gmail.com>
>>>wrote:
>>>
>>>On Fri, Sep 26, 2014 at 10:06 AM, Miguel Angel Salazar de Troya
>>><salazardetroya at gmail.com> wrote:
>>>
>>>That means that if we call SNESSetFunction() we don't build the residual
>>>vector in parallel? In the pflow example
>>>(http://www.mcs.anl.gov/petsc/petsc-as/petsc-current/src/snes/examples/t
>>>u
>>>t
>>>orials/network/pflow/pf.c.html) the function FormFunction() (Input for
>>>SNESSetFunction() works with the local vectors. I don't understand this.
>>>
>>>
>>>
>>>FormFunction() in that link clearly takes in a global vector X and
>>>returns a global vector F. Inside, it
>>>converts them to local vectors. This is exactly what you would do for a
>>>function given to SNESSetFunction().
>>>
>>>  Matt
>>>
>>>
>>>
>>>Thanks
>>>Miguel
>>>
>>>
>>>On Fri, Sep 26, 2014 at 9:34 AM, Matthew Knepley <knepley at gmail.com>
>>>wrote:
>>>
>>>On Fri, Sep 26, 2014 at 9:31 AM, Miguel Angel Salazar de Troya
>>><salazardetroya at gmail.com> wrote:
>>>
>>>Thanks. I had another question about the DM and SNES and TS. There are
>>>similar routines to assign the residual and jacobian evaluation to both
>>>objects. For the SNES case are:
>>>DMSNESSetFunctionLocal
>>>DMSNESSetJacobianLocal
>>>
>>>What are the differences of these with:
>>>
>>>SNESSetFunction
>>>SNESSetJacobian
>>>
>>>
>>>
>>>
>>>SNESSetFunction() expects the user to construct the entire parallel
>>>residual vector. DMSNESSetFunctionLocal()
>>>expects the user to construct the local pieces of the residual, and then
>>>it automatically calls DMLocalToGlobal()
>>>to assembly the full residual. It also converts the input from global
>>>vectors to local vectors, and in the case of
>>>DMDA multidimensional arrays.
>>>
>>>  Thanks,
>>>
>>>    Matt
>>>
>>>
>>>and when should we use each? With "Local", it is meant to evaluate the
>>>function/jacobian for the elements in the local processor? I could get
>>>the local edges in DMNetwork by calling DMNetworkGetEdgeRange?
>>>
>>>Miguel
>>>
>>>
>>>On Thu, Sep 25, 2014 at 5:17 PM, Matthew Knepley <knepley at gmail.com>
>>>wrote:
>>>
>>>
>>>
>>>On Thu, Sep 25, 2014 at 5:15 PM, Miguel Angel Salazar de Troya
>>><salazardetroya at gmail.com> wrote:
>>>
>>>> If you need a symmetric Jacobian, you can use the BC facility in
>>>> PetscSection, which eliminates the
>>>> variables completely. This is how the FEM examples, like ex12, work.
>>>Would that be with PetscSectionSetConstraintDof ? For that I will need
>>>the PetscSection, DofSection, within DMNetwork, how can I obtain it? I
>>>could cast it to DM_Network from the dm, networkdm,  declared in the
>>>main
>>>program, maybe something like this:
>>>DM_Network     *network = (DM_Network*) networkdm->data;Then I would
>>>loop
>>>over the vertices and call PetscSectionSetConstraintDof if it's a
>>>boundary node (by checking the corresponding component)
>>>
>>>
>>>
>>>
>>>I admit to not completely understanding DMNetwork. However, it
>>>eventually
>>>builds a PetscSection for data layout, which
>>>you could get from DMGetDefaultSection(). The right thing to do is find
>>>where it builds the Section, and put in your BC
>>>there, but that sounds like it would entail coding.
>>>
>>>  Thanks,
>>>
>>>     Matt
>>>
>>>
>>>
>>>
>>>Thanks for your responses.Miguel
>>>
>>>
>>>
>>>
>>>On Thu, Sep 25, 2014 at 2:42 PM, Jed Brown <jed at jedbrown.org> wrote:
>>>
>>>Matthew Knepley <knepley at gmail.com> writes:
>>>
>>>> On Thu, Sep 25, 2014 at 1:46 PM, Abhyankar, Shrirang G.
>>>><abhyshr at mcs.anl.gov
>>>>> wrote:
>>>>
>>>>> You are right. The Jacobian for the power grid application is indeed
>>>>> non-symmetric. Is that a problem for your application?
>>>>>
>>>>
>>>> If you need a symmetric Jacobian, you can use the BC facility in
>>>> PetscSection, which eliminates the
>>>> variables completely. This is how the FEM examples, like ex12, work.
>>>
>>>You can also use MatZeroRowsColumns() or do the equivalent
>>>transformation during assembly (my preference).
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>--
>>>Miguel Angel Salazar de Troya
>>>
>>>
>>>Graduate Research Assistant
>>>Department of Mechanical Science and Engineering
>>>University of Illinois at Urbana-Champaign
>>
>>
>>>(217) 550-2360 <tel:%28217%29%20550-2360>
>>>
>>>
>>>salaza11 at illinois.edu
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>--
>>>What most experimenters take for granted before they begin their
>>>experiments is infinitely more interesting than any results to which
>>>their experiments lead.
>>>-- Norbert Wiener
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>--
>>>Miguel Angel Salazar de Troya
>>>Graduate Research Assistant
>>>Department of Mechanical Science and Engineering
>>>University of Illinois at Urbana-Champaign
>>>(217) 550-2360 <tel:%28217%29%20550-2360>
>>>salaza11 at illinois.edu
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>--
>>>What most experimenters take for granted before they begin their
>>>experiments is infinitely more interesting than any results to which
>>>their experiments lead.
>>>-- Norbert Wiener
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>--
>>>Miguel Angel Salazar de Troya
>>>Graduate Research Assistant
>>>Department of Mechanical Science and Engineering
>>>University of Illinois at Urbana-Champaign
>>>(217) 550-2360 <tel:%28217%29%20550-2360>
>>>salaza11 at illinois.edu
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>--
>>>What most experimenters take for granted before they begin their
>>>experiments is infinitely more interesting than any results to which
>>>their experiments lead.
>>>-- Norbert Wiener
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>--
>>>Miguel Angel Salazar de Troya
>>>Graduate Research Assistant
>>>Department of Mechanical Science and Engineering
>>>University of Illinois at Urbana-Champaign
>>>(217) 550-2360 <tel:%28217%29%20550-2360>
>>>salaza11 at illinois.edu
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>--
>>>What most experimenters take for granted before they begin their
>>>experiments is infinitely more interesting than any results to which
>>>their experiments lead.
>>>-- Norbert Wiener
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>--
>>
>>
>>Miguel Angel Salazar de Troya
>>
>>
>>Graduate Research Assistant
>>Department of Mechanical Science and Engineering
>>University of Illinois at Urbana-Champaign
>>(217) 550-2360
>>
>>
>>salaza11 at illinois.edu
>>
>>
>>
>>
>>
>>
>>
>>
>>--
>>Miguel Angel Salazar de Troya
>>Graduate Research Assistant
>>Department of Mechanical Science and Engineering
>>University of Illinois at Urbana-Champaign
>>(217) 550-2360
>>salaza11 at illinois.edu
>
>
>
>
>
>
>
>
>
>-- 
>Miguel Angel Salazar de Troya
>Graduate Research Assistant
>Department of Mechanical Science and Engineering
>University of Illinois at Urbana-Champaign
>(217) 550-2360
>salaza11 at illinois.edu